[gmx-users] CHARMM36 lipid bilayers

Sven Jakobtorweihen Jakobtorweihen at tuhh.de
Thu Oct 21 15:03:51 CEST 2010

Dear gmx-users,

recently Pär Bjelkmar and Thomas Piggot have generated force field files
for Charmm36 lipids. I run some simulations to find the best run
parameters and to check if the results of the original Charmm36 lipid
article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
reproduced with gromacs.

I run 40 ns NPT simulations with semiisotropic pressure coupling
(Parrinello-Rahman, tau_p=5),  the first 10 ns are equilibration and
averages were calculated for the last 30 ns. DMPC and POPC at 303 K and
DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with
pdb2gmx -nochargegrp. All simulations contained 128 lipids and
approximately the same water/lipid ratio (water is TIP3P) as Klauda et
al. I started from charmm27 bilayers provided at the Chramm Gui website.
I used the following parameters:

 rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00;
nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002

These simulations result in the following area per lipid [A^2/lipid]:
DMPC=56.6 +/- 0.4  ; POPC =61.8 +/- 0.4 ;  DPPC=55.0 +/- 0.7

Comparing to the results of Klauda et al (all simulation with the
charmm-package, except one):
DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
+/- 0.4 (with NAMD)

It is obvious that my simulations with gromacs 4.5.1 give lower areas
per lipid for all cases. Considering the deviations observed by Klauda
et al. between Charmm and NAMD simulations ( rvdw_switch was only
changed slightly in NAMD) could lead to the conclusion that DMPC and
POPC are fine. But I am a bit worried about the DPPC result. Did anyone
have suggestions how to improve it? Are these differences expected when
comparing gromacs and charmm simulations? Did by any chance someone else
tested charmm36 bilayers in gromacs?


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